The idea of the approach was not primarily to read the data into a
fixed data structure; but rather to give methods which are by default
empty, but which may be implemented to produce any desired data
structure. Of course, such was also to be made, in particular, one to
produce a molecular structure with data on
multiple chains, secondary structure, bondings, and heterogeneous
elements; though that never happened.

Java download

The main package is the PDB parser package
(no.uio.labmed.pdb.*). This contains two classes, Test and TestParser,
which are runable (implements main) taking a PDB file name as
argument. These two test classes use a helper package to present
results (no.uio.labmed.output.*).

Understanding how to make use of the implementation is perhaps best
done by looking at the Test and TestParser classes: these two are
almost identical. TestParser implements the PDBparser class;
Test implements PDBinterpreter which in turn implements
PDBparser.

The PDBparser class simply parses the PDB file, calling methods for
parsed element (secondary structure element, atom, etc.); extentions
of PDBparser overriding the default methods may then be used to
actually process the data.

The PDBinterpreter class was aimed at helping interpreting the data
from the PDBparser somewhat better, i.e. help organize atoms into
residues etc., but this was never completed.

Download the Java JAR including source files
for the packages no.uio.labmed.pdb.* (the PDB parser) and
no.uio.labmed.output.* (just a simple GUI for use
when developing).

Online documentation (API) for the
pdb and
output packaged (not updated after last
changes).

The packages were made quite some time ago under an older version
of Java, but I have gone over the code just to make it compliant with
Java 5. I'm afraid method and variable names may be interchangably
in English and in Norwegian: at least in the output package.

The pdb package contains the pdb parser classes. The output package
is just a small utility package I made many years ago to help produce
a tabbed window to put information into and not ment to be part of the
parser package, but it was useful to have during development.

If anyone are able to make something useful based on this
package, or instead of this package for that matter, and are prepared
to make it available for others to download, please drop me a hint so
I can link to it: then others coming here to search for a Java PDB
parser package can be directed to something more complete than what I
have to offer here.